Predictive Insights Into Bioactive Compounds from Streptomyces as Inhibitors of SARS-CoV-2 Mutant Strains by Receptor Binding Domain: Molecular Docking and Dynamics Simulation Approaches
| Author | Hourieh Kalhor |
| Author | Mohammad Hossein Mokhtarian |
| Author | Hamzeh Rahimi |
| Author | Behzad Shahbazi |
| Author | Reyhaneh Kalhor |
| Author | Tahereh Komeili Movahed |
| Author | Hoda Abolhasani |
| Accessioned Date | 2024-12-16T01:32:10Z |
| Available Date | 2024-12-16T01:32:10Z |
| Issued Date | 2024-12-31 |
| Abstract | Background: The receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 interacts with the angiotensin-converting enzyme 2 (ACE2) receptor in humans. To date, numerous SARS-CoV-2 variants, particularly those involving mutations in the RBD, have been identified. These variants exhibit differences in transmission, pathogenicity, diagnostics, and vaccine efficacy. Objectives: Although therapeutic agents are currently available to inhibit SARS-CoV-2, most provide supportive and symptomatic relief. Moreover, different variants may exhibit resistance to these treatments. This study aimed to identify a potential compound with favorable antiviral effects against SARS-CoV-2 variants. Methods: The study explored drug discovery through structure-based virtual screening of natural products (NPs) from the StreptomeDB database, targeting the ACE2-binding pocket of the SARS-CoV-2 RBD protein. The analysis included the wild-type protein (PDB ID: 6VW1) as well as the Alpha, Beta, Delta, Lambda, Omicron/BA.1, and Omicron/BA.2 variants. Results: In silico screening identified ‘Stambomycin B’ as a potential compound with the highest binding affinity. Molecular dynamics simulations of the complexes, conducted over 100 ns, confirmed the prediction that ‘Stambomycin B’ could inhibit different SARS-CoV-2 variants effectively. Conclusions: This study concludes that ‘Stambomycin B’, a macrolide compound produced by Streptomycesambofaciens, may be a candidate NP for effectively combating all mutants that occur in the binding of SARS-CoV-2 RBD to ACE2, even those that may arise in the future. |
| DOI | https://doi.org/10.5812/ijpr-150879 |
| URI | https://repository.brieflands.com/handle/123456789/64290 |
| Keyword | SARS-CoV-2 |
| Keyword | ACE2 |
| Keyword | Stambomycin B |
| Keyword | Molecular Docking |
| Keyword | Molecular Dynamics Simulation |
| Publisher | Brieflands |
| Title | Predictive Insights Into Bioactive Compounds from Streptomyces as Inhibitors of SARS-CoV-2 Mutant Strains by Receptor Binding Domain: Molecular Docking and Dynamics Simulation Approaches |
| Type | Research Article |